Arabidopsis thaliana
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REPOSITORIES: ENA
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Project description:Genome-wide analysis of transcription start sites in Arabidopsis planta
| PRJDB5793 | ENA
Project description:Genome-wide analysis of transcription start sites and mRNA translation state in Arabidopsis cells
| PRJDB3455 | ENA
Project description:Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We reported genome-wide high resolution maps of DNase I hypersensitive (DH) sites from both seedling and flower tissues of Arabidopsis from the Columbia (Col) ecotype and the corresponding ddm1 (deficient in DNA methylation 1) mutant. We identified 38,290, 41,193, 38,313, and 38,153 DH sites in leaf (Col), flower (Col), ddm1 leaf, and ddm1 flower tissues, respectively. Approximately 45% of the DH sites in all tissue types were located within 1 kb of a transcription start site (TSS), which represents a putative promoter region. Pairwise comparisons of the DH sites derived from different tissue types revealed DH sites specific to each tissue. DH sites are significantly associated with long non-coding RNAs (lncRNAs) and conserved non-coding sequences (CNSs). The binding sites of MADS-domain transcription factors AP1 and SEP3 are highly correlated with DH sites.
2012-07-06 | GSE34318 | GEO
Project description:Genome-wide identification of nitric-oxide regulated H3K9/14ac sites in Arabidopsis thaliana
| PRJNA323929 | ENA
Project description:Genome-wide identification of FHY3 binding sites in Arabidopsis floral organ (ChIP-Seq)
| PRJNA289556 | ENA
Project description:Genome-wide identification of FHY3 binding sites in Arabidopsis floral organ (RNA-Seq)
| PRJNA289555 | ENA
Project description:eQTL mapping in a F1 diversity panel generated from 111 A.thaliana natural accessions
2011-03-01 | GSE23912 | GEO
Project description:Several studies indicate that plant MIR genes are transcribed by RNA Pol II, similar to what is found in animals (Cai et al., 2004; Lee et al., 2004). By sequencing the 5' transcript ends Xie et al. (2005) mapped the transcription start sites (TSSs) for 52 MIR genes. This list was expanded upon through computational prediction of the core promoters (Zhou et al., 2007). In addition to the TATA box sequence motifs located upstream of the TSSs (Xie et al. 2005), Megraw et al. (2006) identified other transcription factor binding motifs in the promoter of Arabidopsis MIR genes. They showed that within the 800 nucleotides region upstream of TSSs, sequences resembling the binding sites for the transcription factors AtMYC2, ARF, SORLREP3, and LFY were overrepresented relative to protein-coding gene promoters and randomly sampled genomic sequences (Megraw et al. 2006). While these previous studies are instrumental in establishing our working understanding of MIR gene transcription in plants, there are several major knowledge gaps that urgently need to be addressed. Binding of RNA Pol II to the identified MIR promoter regions has not been tested. Because expression of MIR genes does not involve translation, transcriptional control by RNA Pol II might be different from protein-coding genes. In addition, few of the predicted cis elements have been functionally tested. Futher, the number of annotated miRNA genes has since increased from 199 to 232 (miRBase release 17; Kozomara and Griffiths-Jones, 2011). None of the newly identified genes have been subject to examination for promoter and regulatory sequences. Compared to the previously known miRNAs, these genes have narrower phylogenetic distribution and exhibit weaker expression level and more prominent tissue-specific expression (Rajagopalan et al., 2006; Fahlgren et al. 2007; Yang et al., 2011). Based on these observations, it has been argued that continuous gene birth and death allows beneficial miRNAs to be maintained while deleterious ones avoided (Rajagopalan et al., 2006; Fahlgren et al. 2007; Chen and Rajewsky, 2007; Axtell and Bowman, 2008). Identification of the promoter regions of these MIR genes and their comparison to those of the conserved are highly desirable to fully elucidate miRNA based gene regulation. In the current study, we performed chromatin immunoprecipitation (ChIP)-chip for the Pol II complex using the Affymetrix 'At35b_MR_v04' array. We designed a computational approach using genome-wide RPol II binding patterns to identify the promoter region and transcription start site of pri-miRNAs that are actively transcribed.
2012-02-10 | GSE35608 | GEO
Project description:Genomic integrity requires faithful chromosome duplication. Origins of replication are the genomic sites where DNA replication initiates in every cell cycle. There are multiple origins scattered throughout the eukaryotic genome whose genome-wide identification has been a hard challenge, especially in multicellular organisms. Thus, very little is known on the distinctive features of origins in terms of DNA sequence and chromatin context at a genomic scale. As part of a project for profiling replication origins in Arabidopsis thaliana, we have performed ChIP-chip analysis of the binding of ORC1 and CDC6, two proteins involved in initiation of DNA replication. Here, we provide the data of the ORC1-bound and CDC6-bound genomic sites using as control genomic DNA.
2011-02-06 | GSE21928 | GEO